Abstract
Parameter inference in mechanistic models of biopathways based on systems of coupled differential equations is a topical yet computationally challenging problem due to the fact that each parameter adaptation involves a numerical integration of the differential equations. Techniques based on gradient matching, which aim to minimize the discrepancy between the slope of a data interpolant and the derivatives predicted from the differential equations, offer a computationally appealing shortcut to the inference problem. Gradient matching critically hinges on the smoothing scheme for function interpolation, with spurious oscillations in the interpolant having a dramatic effect on the subsequent inference. The present article demonstrates that a time warping approach that aims to homogenize intrinsic functional length scales can lead to a significant improvement in parameter estimation accuracy. We demonstrate the effectiveness of this scheme on noisy data from a dynamical system with periodic limit cycle, and a biopathway model.
Original language | English (US) |
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Title of host publication | Computational Intelligence Methods for Bioinformatics and Biostatistics - 13th International Meeting, CIBB 2016, Revised Selected Papers |
Editors | Giulio Caravagna, Roberto Tagliaferri, David Gilbert, Andrea Bracciali |
Publisher | Springer Verlag |
Pages | 145-159 |
Number of pages | 15 |
ISBN (Print) | 9783319678337 |
DOIs | |
State | Published - 2017 |
Event | 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016 - Stirling, United Kingdom Duration: Sep 1 2016 → Sep 3 2016 |
Publication series
Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 10477 LNBI |
ISSN (Print) | 0302-9743 |
ISSN (Electronic) | 1611-3349 |
Conference
Conference | 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016 |
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Country/Territory | United Kingdom |
City | Stirling |
Period | 09/1/16 → 09/3/16 |
Bibliographical note
Publisher Copyright:© Springer International Publishing AG 2017.
Keywords
- Biopathways
- Differential equations
- Gradient matching
- Optimisation
- Reproducing kernel hilbert space
- Time warping
ASJC Scopus subject areas
- Theoretical Computer Science
- General Computer Science